2024
Bigotti, M.G., Klein, K., Gan, E., Anastasina, M., Andersson, S., Vapalahti, O., Katajisto, P., Erdmann, M., Davidson, A.D., Butcher, S.J. Collinson, I., Ooi, E.E., Balistreri, G., Brancaccio, A., Yamauchi, Y. (2024) The α-dystroglycan N-terminus as an antiviral candidate against SARS-CoV-2 and other enveloped viruses. Antiviral Research 224:105837 https://doi.org/10.1016/j.antiviral.2024.105837. Preprint available at BioRxiv
Füzik, T., *Anastasina, M., Domanska, A., Pulkkinen, L. I. A., Šmerdová, L., Pokorná Formanová, P., Straková, P., Nováček, J., Růžek, D., *Butcher, S.J., *Plevka, P., Assembly and maturation of flaviviruses tolerates deviations from icosahedral arrangement of envelope proteins. (2024) in preparation
Henderikx, RJM, Mann,D, Domanska, A, Dong,J, Shahzad, S, Lak, B, Filopoulou, A., Ludig, D., Grininger, M., Momoh, J., Williams, PA, Laanto, E., Oksanen, H.M., Bisikalo, K., Butcher, SJ, Peters, PJ, Beulen, BWAMM. (2024) VitroJet: new features and case studies. Acta Cryst. Section D80 https://doi.org/10.1107/S2059798324001852
Rosendal, E, Bisikalo, K, Lindgren, M, Willekens, S, Holoubek,J, Svoboda, P, Morini, F, Samuelsson, E, Nordén, R, Růžek, D, Ahlgren, U, Anastasina, M, Butcher, SJ, Nilsson, E, Merits, A, Överby, AK Low-pathogenic chimeric viruses to study the structural proteins of tick-borne encephalitis virus (in preparation)
Shroff, S. Haapakoski M. , Kosti, T., Laajala, M., Leppänen M., Plavec Z., Haapala, A., Butcher, S.J., Ihalainen, J.A., Toppari J., Marjomäki, V. (2024) Antiviral action of a functionalized plastic surface against human coronaviruses. Microbiology Spectrum 12(2):e0300823. doi: 10.1128/spectrum.03008-23
Tammaro, C., Plavec, Z., Myllymäki, L., Mitchell, C., Consalvi, S., Biava, M., Ciogli, A., Domanska, A., Leppilampi V., Buckner, C., Manetto, S., Sciò, P., Coluccia, A., Laajala, M., Marjomäki, V., Butcher, S.J., Poce. G. (2024) Hit optimization of novel coxsackie virus A9 capsid binders. Submitted
2023
Domanska, A., P., Strakov. (2023) The structure of immature tick-borne encephalitis virus. Submitted, preprint available on BioRxiv https://doi.org/10.1101/2023.08.04.551633
, Füzik, T.,
Sah-Teli,S.K., Pinkas, M., Hynönen, Butcher, S.J., Wierenga, R.K, Nováček, J., Venkatesan, R. (2023) Structural basis for the different membrane binding properties of the Escherichia coli anaerobic and human mitochondrial β-oxidation trifunctional enzyme complexes Structure 31:812-825.e6. doi: 10.1016/j.str.2023.04.011
2022
Domanska, A., Plavec, Z., Ruokolainen V., Löflund, B., Marjomäki, V., Butcher, S.J. (2022) Structural studies reveal that endosomal cations promote formation of infectious CVA9 A particles, facilitating RNA and VP4 release. J. Vir. 96:e0136722 DOI: https://doi.org/10.1128/jvi.01367-22 preprint available at BioRxiv doi: https://doi.org/10.1101/2022.09.02.506448
Plavec, Z., Domanska, A., Liu, X., Laine, P., Paulin, L., Varjosalo, M., Auvinen, P., Wolf, S.G., Anastasina, M., Butcher, S.J. (2022) SARS-CoV-2 production, purification methods and UV inactivation for proteomics and structural studies. Viruses 14, 1989. https://doi.org/10.3390/v14091989
Pulkkinen, L.I.A.; Barrass, S.V.; Domanska, A.; Överby, A.K.; Anastasina, M.; Butcher, S.J. Molecular organisation of tick-borne encephalitis virus. (2022) Viruses 14, 792. https://doi.org/10.3390/v14040792. Preprint available at Preprints, 2022040001 (doi: 10.20944/preprints202204.0001.v1)
2021
Barrass, SV, Pulkkinen, LIA, Vapalahti, O., Kuivanen, SH, Anastasina, M., Happonen, L., Butcher, SJ (2021) Proteome-wide cross-linking mass spectrometry to identify specific virus capsid-host interactions between tick-borne encephalitis virus and neuroblastoma cells. bioRxiv 2021.10.29.464531
Flatt, J.W., Domanska, A., Seppälä, A.L., Butcher, S.J. (2021) Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses. Commun Biol 4:250 https://doi.org/10.1038/s42003-021-01779-x Preprint available at BioRxiv: doi: https://doi.org/10.1101/2020.07.06.189373
van Belkum, A., Almeida, C., Bardiaux, B., Barrass, S., Butcher, S.J., Çaykara, T., Chowdhury, S., Datar, R., Eastwood, I., Goldman, A., Goyal, M., Happonen, L., Izadi-Pruneyre, N., Jacobson, T., Johnson, P., Kempf, V.A.J., Kiessling, A., Leva, J., Malik, A., Malmström, J., Meuskens, I., Milner, P., Nilges, M., Pamme, N., Peyman, S., Rodrigues, L., Rodriguez-Mateos, P., Sande, M., Silva, C., Stasiak, A.C., Stehle, T., Thibau, A., Thomsen, M., Vaca, D., Linke D. (2021) Host-pathogen adhesion interactions as the basis of innovative diagnostics for emerging pathogens. Diagnostics 11:1259 https://www.mdpi.com/2075-4418/11/7/1259
2020
Laurinmäki, P., Shakeel, S., Ekström, J., Mohammadi, P., Hultmark, D. , Butcher, S.J. (2020) Structure of Nora virus at 2.7 Å resolution and implications for receptor binding, capsid stability and taxonomy. Scientific Reports 10:19675 https://doi.org/10.1038/s41598-020-76613-1
Saari, H. Turunen, T., Lõhmus, A., Turunen, M., Jalasvuori, M., Butcher, S.J., Ylä-Herttuala, S., Viitala, T., Cerullo, V., Siljander, P.R.M., Yliperttula, M. (2020) Extracellular vesicles provide a capsid-free vector for oncolytic adenoviral DNA delivery. J. Extracellular Vesicles 9:1 https://doi.org/10.1080/20013078.2020.1747206
2019
Abdelnabi, R,. Geraets, J.A., Ma, Y, Mirabelli, C., Flatt, J.W. , Domanska, A., Delang, L., Jochmans, D., Jayaprakash, V., Sinha, B.N., Leyssen, P., Butcher, S.J., Neyts , J. (2019) A novel druggable interprotomer pocket in the capsid of rhino- and enteroviruses. PLoS Biology 17(6):e3000281.
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Domanska, A. Flatt, J.W., Jukonen, J.J.J., Geraets, J.A., Butcher, S.J. (2019) A 2.8- Å resolution cryo-electron microscopy structure of human parechovirus 3 in complex with Fab from a neutralizing antibody. J. Virol 93:e01597-18
Ruokolainen V., Domanska, A., Pellicia, M., Laajala, M., Butcher, S.J., Marjomäki, M. (2019) Extracellular albumin and endosomal ions prime enterovirus particles for uncoating that can be prevented by fatty acid saturation. (2019) J. Virol. 93:e00599-19
Sah-Teli,S.K., Hynönen, M.J., Schmitz, W, Geraets, J.A., Seitsonen, J., Pedersen, J.S., Butcher, S.J., Wierenga, R.K, Venkatesan, R. (2019) Complementary substrate specificity and distinct quaternary assembly of the Escherichia coli aerobic and anaerobic β-oxidation trifunctional enzyme complexes. Biochem J. 476:1975-1994. doi: 10.1042/BCJ20190314.
Wolthers, K., Susi, P., Jochmans, D., Koskinen, J., Landt, O., Sanchez, N., Palm, K., Neyts, K., Butcher, S.J. (2019) Progress in human picornavirus research: new findings from the AIROPico consortium. Antiviral Research 161:100-107. https://doi.org/10.1016/j.antiviral.2018.11.010
2018
Shakeel, S., Evans, J.D., Hazelbaker, M., Kao, C. C., Vaughan, R.C., Butcher, S.J. (2018) Intrinsically-disordered N-termini in human parechovirus 1 capsid proteins bind encapsidated RNA. Scientific Reports 8:5820. doi:10.1038/s41598-018-23552-7
2017
Karelehto, E., van der Sanden, S., Geraets, J.A., Domanska, A., van der Linden, L., Hoogendoorn, D., Koen, G., van Eijk, H., Shakeel, S., Beaumont, T., de Jong, M., Pajkrt, D., Butcher, S.J., Wolthers, K.C. (2017) Strain-dependent neutralization reveals antigenic variation of human parechovirus 3. Scientific Reports 7:12075. doi: 10.1038/s41598-017-12458-5
Patwardhan, A., Brandt, R., Butcher, S.J., Collinson, L., Gault, D., Grünewald, K., Hecksel, C., Huiskonen, J., Iudin, A., Jones, M.L., Korir, P.K., Koster, A., Lagerstedt, I., Lawson, C.L., Mastronarde, D., McCormick, M., Parkinson, H., Rosenthal, P.B., Saalfeld, S., Saibil, H.R., Sarntivijai, S., Solanes Valero, I., Subramaniam, S., Swedlow, J.R., Tudose, I., Winn, M., Kleywegt, G.J. (2017) Building bridges between cellular and molecular structural biology. eLife 6:e25835. doi: 10.7554/eLife.25835
Shakeel, S., Dykeman, E.C., White, S.J., Ora, A., Cockburn, J., Butcher, S.J., Stockley, P.G., Twarock, R. (2017) Genomic RNA folding mediates assembly of human parechovirus. Nature Communications 8:5. doi: 10.1038/s41467-016-0011-z. Direct link to the paper: http://rdcu.be/pybT
2016
Anastasina, M., Le May, N., Bugai, A., Fu, Y., Söderholm, S., Gaelings, L., Ohman, T., Tynell, J., Kyttänen, S., Barboric, M., Nyman, T., Matikainen, S., Julkunen, I., Butcher S.J., Egly, J., Kainov, D. (2016) Influenza virus NS1 protein binds cellular DNA to block transcription of antiviral genes. BBA – Gene Regulatory Mechanisms 1859:1440-8. doi: 10.1016/j.bbagrm.2016.09.005
Shakeel S., Westerhuis B.M., Domanska, A., Konig, R.I., Matadeen, R., Koster, A.J., Bakker, A.Q., Beaumont, T., Wolthers, K.C., Butcher, S.J. (2016) Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis. Nature Communications 7:11387. doi: 10.1038/ncomms11387
2015
Guryanov, S., Liljeroos, L. Kasaragod, P., Kajander, T., Butcher, S.J. (2015) Crystal structure of the measles virus nucleoprotein core in complex with an N-terminal region of phosphoprotein. J. Virol. 90:2849-57. doi: 10.1128/JVI.02865-15
Shakeel S., Westerhuis B.M., Ora, A., Koen, G., Bakker, A.Q., Claassen, Y., Wagner, K., Beaumont, T., Wolthers, K.C., Butcher, S.J. (2015) Structural basis of human parechovirus neutralization by human monoclonal antibodies. J. Virol. 89:9571-80. doi: 10.1128/JVI.01429-15
2014
Anastasina, M., Terenin, I., Butcher, S.J., Kainov, D.E. (2014) A technique to increase protein yield in a rabbit reticulocyte lysate translation system. BioTechniques 56:36-9. doi: 10.2144/000114125
Hattula, K., Hirschberg, D., Kalkkinen, N., Butcher, S.J., Ora, A. (2014) Association between the intrinsically disordered protein PEX19 and PEX3. PLOS ONE 9:e103101. doi: 10.1371/journal.pone.0103101
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Hetzel, U., Sironen, T., Laurinmäki, P., Liljeroos, L., Patjas, A., Henttonen, H., Vaheri, A., Artelt, A., Kipar, A., Butcher, S.J., Vapalahti, O., Hepojoki, J. (2014) Reply to “Updated phylogenetic analysis of arenaviruses detected in boid snakes”. J. Virol. 88:1401.
Magarkar, A., Mele, N., Abdel-Rahman, N., Butcher, S., Torkkeli, M., Serimaa, R., Paananen, A., Linder, M., Bunker, A. (2014) Hydrophobin film structure for HFBI and HFBII and mechanism for accelerated film formation. PLOS Computational Biology 10:e1003745. doi: 10.1371/journal.pcbi.1003745
Pandurangan, A.P., Shakeel, S., Butcher, S.J., Topf M. (2014) Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change. J. Struct. Biol. 185:427-39.
Patwardhan, A., Ashton, A., Brandt, R., Butcher,S., Carzaniga, R., Chiu, W., Collinson, L., Doux, P., Duke, E., Ellisman, M., Franken, E., Grünewald, K., Heriche, J., Koster, A., Kühlbrandt, W., Lagerstedt, I., Larabell, C., Lawson,C.L., Saibil, H.R., Sanz-García,E., Subramaniam, S., Verkade, P., Swedlow, J.R., Kleywegt, G.J. (2014) A 3D cellular context for the macromolecular world. Nat. Struct. Mol. Biol. 21:841-5.
Weinheimer, I., Boonrod,K., Moser, M., Wassenegger,M., Krczal, G., Butcher, S.J., Valkonen, J.P.T. (2014) Binding and processing of small dsRNA molecules by the Class 1 RNase III protein encoded by sweet potato chlorotic stunt virus. J. Gen. Virol. 95:486-95.
2013
Happonen, L., Oksanen, E., Liljeroos, L., Goldman, A., Kajander, T., Butcher, S.J. (2013) The structure of the NTPase that powers DNA packaging into Sulfolobus turreted icosahedral virus 2. J. Virol. 87:8388-98.
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Hedegaard, S., Nilsson, C., Laurinmäki, P., Butcher, S.J., Urtti, A., Yaghmur, A. (2013) Nanostructured aqueous dispersions of citrem interacting with lipids and PEGylated lipids. RSC Advances 3:24576–24585.
Hetzel, U., Sironen, T., Laurinmäki, P., Liljeroos, L., Patjas, A., Henttonen, H., Vaheri, A., Artelt, A., Kipar, A., Butcher, S.J., Vapalahti O., Hepojoki J. (2013) Isolation, identification and characterization of novel Arenaviruses, the etiological agent of Boid Inclusion Body Disease. J. Virol. 87:20 10918-35.
Hirvonen, S, Karesoja, M., Karjalainen, E., Hietala, S., Laurinmäki, P., Vesanen, E., Butcher, S.J., Tenhu, H. (2013) Colloidal properties and gelation of aqueous dispersions of conductive poly(benzimidazobenzophenanthroline) derivatives. Polymer 54:694-701.
Karjalainen, E., Chenna, N., Laurinmäki, P., Butcher, S.J., Tenhu H. (2013) Diblock copolymers consisting of polymerized ionic liquid and poly(N-isopropylacrylamide). Effects of PNIPAM block length and counter ion on self-assembling and thermal properties. Polym. Chem. 4:1014-24.
Liljeroos, L., Krzyzaniak, M., Helenius, A., Butcher, S.J. (2013), Architecture of respiratory syncytial virus revealed by electron cryotomography. Proc. Natl. Acad. Sci. (USA) 110:11133-11138.
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Nilsson, C., Barrios-Lopez, B., Kallinen, A., Laurinmӓki, P., Butcher, S.J., Raki, M., Bergstrӧm, K., Weng Larsen, S., Østergaard, J., Larsen, C., Urtti, A., Airaksinen, A., Yaghmur, A. (2013) SPECT/CT imaging of radiolabeled cubosomes and hexosomes for potential theranostic applications. Biomaterials 34:8491-503.
Pietilä, M.K., Laurinmäki, P., Russell, D.A., Ko, C., Jacobs-Sera, D., Butcher, S.J., Bamford, D.H., Hendrix, R.W. (2013) Insights into head-tailed viruses infecting extremely halophilic archaea. J. Virol. 87:3248-60.
Pietilä, M.K., Laurinmäki, P., Russell, D.A., Ko, C., Jacobs-Sera, D., Hendrix, R.W., Bamford, D.H., Butcher, S.J. (2013) Structure of the archaeal head-tailed virus HSTV-1 completes the HK97-fold story. Proc. Natl. Acad. Sci. (USA) 110:10604-9.
Pšenčík, J., Arellano, J.M., Collins, A.M., Laurinmäki, P., Torkkeli, M., Löflund, B., Serimaa, R.E., Blankenship, R.E., Tuma, R., Butcher, S.J. (2013) Structure and functional role of carotenoids in chlorosomes. J. Bact 195:1727-34.
Shakeel, S., Seitsonen, J., Kajander, T., Laurinmäki, P., Hyypiä, T., Susi, P., Butcher, S.J. (2013) Structural and functional analysis of coxsackievirus A9 receptor binding and uncoating. J. Virol. 87:3943-51.
Comment by MDLinx http://www.mdlinx.com/infectious-disease/news-article.cfm/4501390
2012
Dearborn, A.D., Laurinmäki, P., Chandramouli, P., Rodenburg, C.M., Wang, S., Butcher, S.J., Dokland, T. (2012) Structure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations. J. Struct. Biol. 178:215-24.
Koho, T., Huhti, L., Blazevic, V., Nurminen, K., Butcher, S.J., Laurinmäki, P., Kalkkinen, N., Rönnholm, G., Vesikari, T., Hytönen, V.P., Kulomaa, M.S. (2012) Production and characterization of virus-like particles and the P domain protein of GII.4 norovirus. J. Vir. Methods 179:1-7.
Koho, T., Mäntylä,T., Laurinmäki, P., Huhti, L. Butcher, S., Vesikari,T., Kulomaa, M.S., Hytönen, V.P. (2012) Purification of norovirus-like particles (VLPs) by ion exchange chromatography. J. Vir. Methods. 181:6-11.
Manole, V., Laurinmäki, P., Van Wyngaardt, W., Potgieter, C.A., Wright, I.M, Venter, G.J., van Dijk, A.A., Sewell, B.T., Butcher, S.J. (2012) Structural insight into African horsesickness virus infection. J. Virol. 86:7858-66.
Pietilä, M.K., Atanasova, N.S., Manole, V., Liljeroos, L., Butcher, S.J., Oksanen, H.M., Bamford, D.H. (2012) Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J. Virol. 86:5067-79.
Sarin, L.P, Hirvonen, J., Laurinmäki, P., Butcher, S.J., Bamford, D.H., Poranen, M.M. (2012) Bacteriophage ϕ6 nucleocapsid surface protein 8 interacts with virus-specific membrane vesicles containing the major envelope protein 9. J. Virol. 86:5376-79.
Seitsonen, J., Shakeel, S., Susi, P., Pandurangan, A., Sinkovits, R.S., Hyvönen, H., Laurinmäki, P., Ylä-Pelto, J., Topf, M., Hyypiä, T., Butcher, S.J. (2012) Structural analysis of coxsackievirus A7 reveals conformational changes associated with uncoating. J. Virol. 86:7207-15.
Skurnik, M., Hyytiäinen, H., Happonen, L., Kiljuenn, S., Datta, N., Mattinen, L., Williamson, K., Kristo, P., Szeliga, M., Kalin-Mänttätri, L., Ahola-Iivarinen, E., Kalkkinen, N., Butcher S.J. (2012) Characterization of the genome, proteome and structure of yersiniophage φR1-37. J. Virol. 86:12625-42.
2011
Alhoranta, A., Lehtinen, J., Urtti, A., Butcher, S.J., Aseyev, V., Tenhu, H. (2011) Cationic amphiphilic star and linear block copolymers: synthesis, self-assembly and in vitro gene transfection. Biomacromolecules 12:3213-22.
Dichlberger, A., Schlager, S., Lappalainen, J., Käkelä, R., Hattula, K., Butcher, S.J., Schneider, W.J., Kovanen, P.T. (2011) Lipid body formation during maturation of human mast cells. J. Lipid Research 52:2198-208.
Kumar, V., Butcher, S.J., Öörni, K., Engelhardt, P., Heikkonen, J., Kaski, K., Ala-Korpela, M., Kovanen, P.T. (2011) Three-dimensional cryoEM reconstruction of native LDL particles to 16Å resolution at physiological body temperature. PLoS ONE 6:e18841. doi:10.1371/journal.pone.0018841.
Leo, J.C., Lyskowski A., Hattula, K., Hartmann, M.,Schwarz, H., Butcher, S.J., Linke, D., Lupas, A.N., Goldman, A. (2011) The structure of E. coli IgG-binding protein D suggests a general model for bending and binding in trimeric autotransporter adhesins. Structure 19:1021-30.
Liljeroos, L., Huiskonen, J., Ora, A., Susi, P., Butcher, S.J. (2011) Electron cryotomography of measles virus reveals that matrix protein coats the ribonucleocapsid within intact virions. Proc. Natl. Acad. Sci. (USA) 108:18085-90.
2010
Happonen, L.J., Redder, P., Peng, X., Reigstad, L.J., Prangishvili, D., Butcher, S.J. (2010) Familial relationships in hyperthermo- and acidophilic archaeal viruses. J. Virol. 84:4747-54.
Huiskonen, J.T., Hepojoki, J., Laurinmäki, P., Vaheri, A., Lankinen. H., Butcher, S.J., Grunewald, K. (2010) Electron cryo-tomography of tula hantavirus suggests a unique assembly paradigm for enveloped viruses. J. Virol. 84:4889-97.
Ora, A., Oksanen, E., Kajander, T., Goldman, A., Butcher, S.J. (2010) Crystallisation and preliminary crystallographic analysis of mouse peroxiredoxin II with significant pseudosymmetry. Acta Crystallogr. F 66:357-60.
Paasonen, L. Sipilä, T., Subrizi, A., Laurinmäki, P., Butcher, S.J., Rappolt, M., Yaghmur, A., Urtti, A., Yliperttula, M. (2010) Gold-embedded photosensitive liposomes for drug delivery: triggering mechanism and intracellular release. J. Controlled Release 147:136-43.
Seitsonen, J., Susi, P., Heikkilä, O., Sinkovits, R.S., Laurinmäki, P., Hyypiä, T., Butcher, S.J. (2010) Interaction of αVβ3 and αVβ6 integrins with Human parechovirus 1. J. Virol 84:8509-19.
2009
Polianskyte, Z., Peitsaro, N., Dapkunas, A., Liobikas, J., Soliymani, R., Lalowski, M., Speer, O., Seitsonen, J., Butcher, S., Cereghetti, G.M., Linder, M.D., Merckel, M., Thompson, J., Eriksson, O. (2009) LACTB is a filament-forming protein localized in mitochondria Proc. Natl. Acad. Sci. (USA) 106:18960-5.
Psencik, J., Collins, A.M., Liljeroos, L.,Torkkeli, M., Laurinmäki, P., Ansink, H.M., Ikonen, T.P., Serimaa, R.E., Blankenship, R.E., Tuma, R., Butcher, S.J. (2009) Structure of chlorosomes from the green filamentous bacterium Chloroflexus aurantiacus. J. Bact. 191:6701-8.
Saarikangas, J., Zhao, H., Pykäläinen, A., Laurinmäki, P., Mattila, P., Kinnunen, P., Butcher, S.J., Lappalainen, P. (2009) Molecular mechanisms of membrane deformation by I-BAR domain proteins. Current Biology 19:95-107.
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2008
Abrescia, N.G.A., Grimes, J.M., Kivelä, H.M. Assenberg, R., Sutton, G., Butcher, S.J. Bamford, J.K., Bamford, D.H., Stuart, D.I. (2008) Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. Mol. Cell. 31:749-61.
Arellano, J.B., Torkkeli, M., Tuma, R., Laurinmäki, P., Melø, T.B., Ikonen, T.P., Butcher, S.J., Serimaa, R.E., Psencik, J. (2008) Hexanol-induced order-disorder transitions in lamellar self-assembling aggregates of bacteriochlorophyll c in Chlorobium tepidum chlorosomes. Langmuir 24:2035-41.
Jaatinen, S.T., Happonen, L.J., Laurinmäki, P., Butcher, S.J., Bamford, D.H. (2008) Biochemical and structural characterisation of membrane-containing icosahedral dsDNA bacteriophages infecting thermophilic Thermus thermophilus. Virology 379:10-19. Erratum in: Virology 427:224.
Jäälinoja, H.T., Roine, E., Laurinmäki, P., Kivelä, H.M., Bamford, D.H., Butcher, S.J. (2008) Structure and host cell interaction of SH1, a lipid-containing, halophilic euryarchaeal virus. Proc. Natl. Acad. Sci. (USA) 105:8008-13.
Lindén, M.V., Meinander, K., Helle, A., Yohannes, G., Riekkola, M., Butcher, S.J., Viitala T., Wiedmer, S.K. (2008) Characterization of phosphatidylcholine/ poly(ethylene glycol)-lipid aggregates and their use as coatings and carriers in capillary electrophoresis. Electrophoresis 29:852-62.
Poranen, M.M., Butcher, S.J., Simonov, V.M., Laurinmäki, P., Bamford, D.H. (2008) Roles of the minor capsid protein P7 in the assembly and replication of dsRNA bacteriophage phi6. J. Mol. Biol. 383:529-38.
Seitsonen, J.J.T., Susi, P. Lemmetty, A., Butcher, S.J. (2008) Structure of the mite-transmitted blackcurrant reversion nepovirus using electron cryomicroscopy. Virology 378:162-8.
Strandman S., Zarembo A., Darinskii A.A., Laurinmäki P, Butcher S.J., Vuorimaa, E., Lemmetyinen, H., Tenhu, H. (2008) The effect of the number of arms on the association of amphiphilic star block copolymers. Macromolecules 41:8855-64.
2007
Huiskonen, J.T., Jäälinoja, H.T., Briggs, J.A.G., Fuller, S.D., Butcher, S.J. (2007) Structure of a hexameric RNA packaging motor in a viral polymerase complex. J. Struct. Biol. 158:156-64.
Huiskonen, J.T., Manole, V., Butcher, S.J. A tale of two spikes in bacteriophage PRD1. Proc. Natl. Acad. Sci. (USA) 104:6666-71.
Ikonen, T.P., Li, H., Psencik, L., Laurinmäki, P., Butcher, S.J. Frigaard, N., Serimaa, R.E., Bryant, D.A., Tuma, R. (2007) X-ray scattering and electron cryomicroscopy study on the effect of carotenoid biosynthesis to the structure of Chlorobium tepidum chlorosomes. Biophys. J. 93:620-8.
Jäälinoja, H.T., Huiskonen, J.T., Butcher, S.J. (2007) Electron cryo-microscopy comparison of the architectures of the enveloped bacteriophages φ6 and φ8. Structure 15:157-67.
Strandman S., Zarembo A., Darinskii A.A., Löflund B, Butcher S.J., Tenhu, H. (2007) Self-assembling of star-like amphiphilic block copolymers with polyelectrolyte blocks. Effect of pH. Polymer 48:7008-16.
2006
Huiskonen, J.T., de Haas, F., Bubeck, D., Bamford, D.H., Fuller, S. D., Butcher, S.J. (2006) Structure of the bacteriophage φ6 nucleocapsid suggests a mechanism for sequential RNA packaging. Structure 14:1039-48.
Psencik, L., Arellano, J. B., Ikonen, T.P., Borrego, C. M., Laurinmäki, P., Butcher, S.J., Serimaa, R.E., Tuma, R. (2006) Internal structure of chlorosomes from brown-coloured Chlorobium species and the role of carotenoids in their assembly. Biophys J. 91: 1433-40.
Strandman, S., Hietala, S., Koli, B., Butcher, S.J., Tenhu, H. (2006) Supramolecular assemblies of amphiphilic PMMA-b-PAA stars in aqueous solutions. Polymer 47:6524-35.
2005
Briggs, J.A.G., Huiskonen, J.T., Fernando, K.V., Gilbert, R.J.C., Scotti, P., Butcher, S.J., Fuller, S.D. (2005) Classification and three-dimensional reconstruction of unevenly distributed or symmetry mismatched features of icosahedral particles. J. Struct. Biol. 150:332-9.
Laurinmäki, P.A., Huiskonen, J.T., Bamford, D.H., Butcher, S.J. (2005) Membrane proteins modulate bilayer curvature in the membrane-containing bacterial virus Bam35. Structure 13:1819-28.
Comments by Faculty 1000 at Faculty of 1000
2004
Abrescia, N.G.A., Cockburn, J.J.B., Grimes, J.M., Sutton, G.C., Diprose, J.M., Butcher, S.J., Fuller, S.D., San Martin, C., Burnett, R., Stuart, D.I., Bamford, D.H., Bamford J.K.H. (2004) Insights into assembly from structural analysis of bacteriophage PRD1. Nature 432:68-74.
Comments by Faculty 1000 at Faculty of 1000
Huiskonen, J.T., Kivelä, M. H., Bamford, D.H., Butcher S.J. (2004) The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes. Nature Struct. Mol. Biol. 11:850-6.
Comments by Faculty 1000 at Faculty of 1000
Psencik, L., Ikonen, T.P., Laurinmäki, P., Merckel, M.C., Butcher, S.J. Serimaa, R.E., Tuma, R. (2004) Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria. Biophysical J. 87:1165-72.
Salgado, P.S., Makeyev, E.V., Butcher, S.J., Bamford, D.H., Stuart, D.I., Grimes, J.M. (2004) The structural basis for RNA specificity and calcium inhibition of an RNA-dependent RNA polymerase. Structure 12:307-16.
2003
Doan, D., Lee, K.C., Laurinmäki, P., Butcher, S.J., Wong, S., Dokland, T. (2003) Three-dimensional reconstruction of Hibiscus chlorotic ringspot virus. J. Struct. Biol. 144:253-61.
Kainov, D.E., Butcher, S.J., Bamford, D.H., Tuma, R. (2003) Conserved intermediates on the assembly pathway of dsRNA bacteriophages. J. Mol. Biol. 328:791-804.
Kainov, D.E., Pirttimaa, M., Tuma, R., Butcher, S.J., Thomas, G.J., Bamford, D.H., Makeyev, E.V. (2003) RNA packaging device of dsRNA bacteriophages: possibly as simple as hexamer of P4 protein. J. Biol. Chem 278:48084-91.
Wang, S., Chandramouli, P., Butcher, S.J., Dokland, T. (2003) Cleavage leads to expansion of bacteriophage P4 procapsids in vitro. Virology 314:1-8.
Xu, L., Benson, S.D., Butcher, S.J., Bamford, D.H., Burnett, R.M. (2003) The receptor-binding protein, P2 of PRD1, a virus targeting antibiotic-resistant bacteria, has a novel fold suggesting multiple functions. Structure 11:309-22.
Yang, H., Makeyev, E. V., Butcher, S.J., Gaidelyte, A., Bamford, D.H. (2003) Two distinct mechanisms ensure transcriptional polarity in dsRNA bacteriophages. J. Virology 77:1195-203.
2002
San Martin, C., Huiskonen, J., Bamford, J. K. H., Butcher, S.J., Fuller, S.D., Bamford, D.H., Burnett, R. (2002) Minor proteins, mobile arms and membrane-capsid interactions in bacteriophage PRD1 capsid. Nature Structural Biology 9:756-63.
Comments by Faculty 1000 at Faculty of 1000
2001
San Martin, C., Burnett, R., de Haas, F., Heinkel, R., Rutten, T., Fuller, S.D., Butcher, S.J., Bamford, D.H. (2001) Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1, and shows key capsid and membrane interactions. Structure 9:917-30.
Comments by Faculty 1000 at Faculty of 1000
Butcher, S.J., Grimes, J.M., Makeyev, E.V., Bamford, D.H., Stuart, D.I. (2001) A mechanism for initiating RNA-dependent RNA polymerization. Nature 410:235-40.
2000
Butcher, S.J., Makeyev, E.V., Grimes, J.M., Stuart, D.I., Bamford, D.H. (2000) Crystallization and preliminary X-ray crystallographic studies on the bacteriophage ø6 RNA-dependent RNA polymerase. Acta Crystallogr. D 56:1473-5.
Xu, L., Butcher, S.J., Benson, S.D., Bamford, D.H., Burnett, R.M. (2000) Crystallization and preliminary X-ray analysis of receptor-binding protein P2 of bacteriophage PRD1. J. Struct. Biol. 131:159-63.
1999
Rydman, P.S., Caldentey, J., Butcher, S.J., Fuller, S.F. Rutten, T., Bamford, D.H. (1999) Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex J. Mol. Biol. 291:575-87.
1998
Butcher, S.J., Aitken, J. Mitchell, J., Gowen, B., Dargan, D. (1998) Structure of the human cytomegalovirus B capsid by electron cryomicroscopy and image reconstruction J.Struct. Biol. 124:70-6.
1997
Butcher, S.J., Dokland, T.D., Ojala, P., Bamford, D.H., Fuller, S.D. (1997) Intermediates in the assembly pathway of the double stranded RNA virus ø6. EMBO J. 16:4477-87.
Palmer, K., Tichelaar, W., Myers, N., Burns, N.R., Butcher, S.J., Kingsman, A.J., Fuller, S.D., Saibil, H.R. (1997) Cryo-EM structure of yeast Ty retrotransposon virus-like particles. J. Virology 71:6863-8.
1996
Fuller, S.D., Butcher, S.J., Cheng, R.H., Baker, T.S. (1996) Three-dimensional reconstruction of icosahedral particles-The uncommon line. J. Struc. Biol. 116:48-55.
1995
Butcher, S.J., Bamford, D.H., Fuller, S.D. (1995) DNA packaging orders the membrane of bacteriophage PRD1. EMBO J. 14:6078-86.
Fuller, S.D., Berriman, J., Butcher, S.J., Gowen, B.E. (1995). Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex. Cell 81:715-72.
Kirillov, M.Yu., Shumakov, Yu.L., Nechaeva, E.V., Butcher, S., Sinjashina, L., Runeberg, K., Romantschuk, M., Karataev, G.I. (1995) Repeated sequences isolated from Bordatella pertussis induceDNA-rearrangements and deletions at high frequency. Gene 166:111-6.
Muttilainen, S., Butcher, S., Runeberg, K., Nurminen, M., Idänpään-Heikkilä, I., Wahlström, E., Sarvas, M. (1995) Heterologous production of the P1 porin of Neisseria meningitidis in Bacillus subtilis: the effect of an N-terminal extension on the presentation of native-like epitopes. Microb. Pathogen. 18:365-71.
1993
Luo, C., Butcher, S., Bamford, D.H. (1993) Isolation of a phospholipid-free protein shell of bacteriophage PRD1, an E.coli virus with an internal membrane. Virology 194:564-9.
Shumakov, Yu.L., Kirillov, M.Yu., Butcher, S., Nechaeva, E.V., Runibergnyuman, K, Sinjashina, L.N., Karataev, G.I. (1993) Nucleotide sequence and properties of a transposon-like structure from the chromosome of Bordatella pertussis. Genetika, 29:1061-9. (In Russian)
1992
Nurminen, M., Butcher, S., Idänpään-Heikkilä, I., Wahlstöm, E., Muttilainen, S., Runeberg-Nyman, K., Sarvas, M., Mäkelä, P.H. (1992) The class 1 outer membrane protein of Neisseria meningitidis produced in Bacillus subtilis can give rise to protective immunity. Molecular Microbiology 6:2499-506.
1991
Butcher, S., Sarvas, M., Runeberg-Nyman, K. (1991) Class-3 porin protein of Neisseria meningitidis: cloning and structure of the gene. Gene 105:125-8.
Puohiniemi, R., Butcher, S., Tarkka, E., Sarvas, M. (1991) High level production of Escherichia coli outer membrane proteins OmpA and OmpF intracellularly in Bacillus subtilis. FEMS Microbiology Letters 83:29-33.
Proceedings
Arellano, J., Torkkeli, M., Pšenčik, J., Laurinmäki, P., Butcher, S.J., Serimaa, R.E., Tuma, R. (2007) Effect of the hexanol treatment on the organization of bacteriochlorophyll aggregates in Chlorobium tepidum chlorosomes. Biophysical J. 505A-505A Suppl. S.
Arellano, J.B., Borrego, C.M., Butcher, S.J., Ikonen, T., Laurinmäki, P., Pšenčik, J., Serimaa, R.E., Tuma, R. (2005) Lamellar pigment arrangement in chlorosomes from green sulfur bacteria and role of carotenoids in assembly. Biophysical J., 88:175A-175A Part 2 Suppl. S
Butcher, S., Koistinen T., Väisänen, E. (1992) The growth of contaminating lactobacilli and alcohol or baker’s yeast production organisms under inhibitory conditions. Proceedings of the COMETT course on microbial contaminants, Helsinki 1991 and 1992. Ed. by M. Korjola and V. Backström. Foundation for Biotechnical and Industrial Fermentation Research 7 :99-130
Butcher, S.J., Omar, P.J., Sarvas, M., Runeberg-Nyman, K. (1990). Sequence comparisons of class 1 genes from Neisseria meningitidis and a folding model of the class 1 protein, p. 193-198. In M. Achtman, P. Kohl, C. Marchal, G. Morelli, A. Seiler, and B. Thiesen (ed.), Neisseriae 1990. Walter de Gruyter, Berlin, Germany.
Pšenčik, J., Laurinmäki, P., Butcher, S., Serimaa, R., Tuma, R. (2007) Changes in the lamellar organization of bacteriochlorophyll aggregates in chlorosomes upon hexanol treatment. Photosynthesis Research, 91:170-171 PS356
Pšenčik, J., Laurinmäki, P., Ikonen, T., Merckel, M., Butcher, S.J., Serimaa, R.E., Tuma, R. (2004) Cryo-electron microscopy and X-ray scattering reveal novel pigment arrangement within the chlorosome, the light harvesting apparatus of green photosynthetic bacteria. Biophysical J. 86:12A-12A Part 2 Suppl. S.
Suchanova, B., Manole, V., Kang, S., Happonen, L., Ora, A., Prevelige, P., Butcher, S., Tuma, R. (2007) Protein dynamics and assembly of dsRNA bacteriophage by hydrogen/deuterium exchange detected by mass spectrometry. Molecular and Cellular Proteomics 6:26-26 Suppl. S.
Monographs
Butcher, S.J. (1995) The three dimensional structure of the membrane-containing bacteriophage, PRD1. PhD Thesis, University of London.
Reviews & popular science articles
Plavec, Z., Pöhner, I., Poso, A., Butcher, S.J. (2021) Virus structure and structure-based antivirals. Current Opinion in Virology 51:16-24 https://doi.org/10.1016/j.coviro.2021.09.005
Domanska, A., Guryanov, S., Butcher, S.J. (2021) A comparative analysis of parechovirus protein structures with other picornaviruses. Open Biology 11: 210008 https://doi.org/10.1098/rsob.210008
Barrass, S.V, Butcher, S.J. (2020) Advances in high throughput methods for the identification of virus receptors. Med Microbiol Immunol. 209:309–323
Flatt, J.W., Butcher, S.J. (2019) Adenovirus flow in host cell networks. Open Biology 9: 190012 http://dx.doi.org/10.1098/rsob.190012
Pulkkinen, L. (2018) Kryoelektronimikroskopia mullistaa molekyylibiologian. Natura 1/18:30-33 http://www.naturalehti.fi/2018/03/23/kryoelektronimikroskopia-mullistaa-molekyylibiologian/
Pulkkinen, L.I.A, Butcher, S.J., Anastasina, M. (2018) Tick-borne encephalitis virus: a structural view. Viruses 10:350. doi: 10.3390/v10070350
Anastasina, M., Domanska, A., Palm, K., Butcher, S.J. (2017) Human picornaviruses associated with neurological diseases and their neutralization by antibodies. Journal of General Virology, 98:1145-58. doi: 10.1099/jgv.0.000780
Happonen, L.J., Erdmann, S., Garrett R.A., Butcher S.J. (2014) Adenosine triphosphatases of thermophilic, archaeal double-stranded DNA viruses. Cell & Biosciences 4:37. doi: 10.1186/2045-3701-4-37. eCollection.
Liljeroos, L., Butcher, S.J. (2013) Matrix proteins as centralized organisers of negative-sense RNA virions. Frontiers in Bioscience 18:696-715.
Huiskonen, J.T., Butcher, S.J. (2007) Membrane-containing viruses with icosahedrally symmetric capsids. Current Opinion in Structural Biology 17:229-36.
Bamford, D., Butcher, S. (2002) Menetelmien yhdistäminen paljasti virusten sukulaisuuden Kemia-Kemi 29:42-3.
Book Chapters
Tuma, R, Butcher, S.J., Oksanen, H.O. (2020) Membrane-containing icosahedral DNA bacteriophages. In “Encyclopedia of Virology” 4th Edition Ed. (accepted)
Pšenčik, J., Butcher, S.J., Tuma, R. (2014) Chlorosomes: Structure, function and assembly. In “The structural basis of biological energy generation.”Ed- Hohmann-Marriott, Springer Science+Business Media, New York.
Butcher, S.J., Manole, V., Karhu, N.J. (2012) PRD1 assembly. In “Viral Molecular Machines” Ed. M. G. Rossmann and V. Rao, Springer Science+Business Media, New York. p. 365-377
Bamford, J.K.H., Butcher, S.J. (2008) Icosahedral dsDNA bacteriophages with an internal membrane. In “Encyclopedia of Virology” 3rd Edition Ed. B.W.J. Mahy & M.H.V. Van Regenmortel, Elsevier Ltd. Vol 3, p 1-6
Grahn, A.M., Butcher, S., Bamford, J.K.H., Bamford, D.H. (2006) PRD1 – dissecting the genome, structure and entry. In “The Bacteriophages” Ed. R. Calendar. Oxford University Press, New York. p.161-170
Butcher, S.J. (2003) The devil is in the detail – uncovering atomic details of the membrane-containing virus PRD1 by a combination of cryo-electron microscopy, image reconstruction and X-ray diffraction. In “CSC Report on Scientific Computing 2001-2003” Eds. S. Kotila, J. Haataja, P. Forsström, J. Ignatius, L. Jukka, M. Laine, N. Runeberg, P. Råback, and V. Savolainen, CSC
PhD Theses
Zlatka Plavec. Stay closed sesame: Structural analysis of virus capsid conformations using cryo-EM and implications for treatment development. University of Helsinki, submitted
Lauri I.A. Pulkkinen. Strong in the real way: protein-protein and protein-lipid interactions in tick-borne encephalitis virus stability and assembly. University of Helsinki, November 2022
Sarah Barrass. Molecular organisation and host-cell interactions of tick-borne encephalitis virus. What makes the virus tick? University of Helsinki, July 2022
Pasi Laurinmäki. Cryo-EM in structural virology: dissecting the icosahedral capsid. University of Helsinki, May 2020
Maria Anastasina. Influenza A virus-host interactions and their control by viral non-structural protein NS1. University of Helsinki, April 2015
Shabih Shakeel. Human picornaviruses: uncoating, assembly and interactions with cellular receptors. University of Helsinki, April 2014
Lassi Liljeroos. Capsids, matrices and vesicles – structural insights into the assembly of Paramyxoviruses, University of Helsinki, October 2013
Violeta Manole. Structural studies on viral receptor-binding proteins. University of Helsinki, September 2012
Lotta J. Happonen. Life on the edge:structural studies of the extremophilic viruses P23-77 and STIV2. University of Helsinki, June 2012
Jani J.T. Seitsonen. Structural studies on members of the Picornavirus superfamily. University of Helsinki, February 2011
Harri T. Jäälinoja. Electron cryo-microscopy studies of bacteriophage phi8 and archaeal virus SH1. University of Helsinki, February 2007
Juha T. Huiskonen. Structure and assembly of membrane-containing dsDNA bacteriophages. University of Helsinki, December 2005
MSc Theses
Markus Mustonen, University of Helsinki
Cienna Buckner. 3D reconstruction of Coxsackievirus A9 in complex with antiviral compound CL301. University of Helsinki 2024
Cristopher Mitchell. Antiviral inhibition of coxsackievirus A9 solved using cryogenic electron microscopy and image processing. University of Helsinki 2024
Kyrylo Bisikalo, The chimeric Langat/Tick-borne encephalitis virion structure presents native epitopes for antiviral development. University of Helsinki 2023
Salla Panka, Isolation and characterization of new bacteriophages against clinical Klebsiella pneumoniae strains. University of Helsinki 2023
Pinja Pikkarainen. Mikrobiologian opetus ja sen tutkimuksellisuus yläkoulussa. University of Helsinki. 2023
Valtteri Lemppilampi. Infection inhibition and structural characterization of coxsackievirus A9 in complex with compound CL213. University of Helsinki January 2023
Lotta Riihimäki. Optimization and validation of gene-expression knockdown to inhibit SARS-CoV-2 infection. University of Helsinki, December 2022
Johanna Göransson. Mikrobiologian tehtävät ja niiden tutkimuksellisuus yläkoulun biologian oppikirjoissa. University of Helsinki, June 2022
Alma Seppälä. Structure of rhinovirus A9 and infection inhibition with benzene sulfonamide derivatives. University of Helsinki, May 2021
Zlatka Plavec. Investigation of antiviral activity of posaconazole against Parechoviruses, University of Helsinki, April 2019
Hussein Alburkat. Characterization of novel LCMV strains in Southern Iraq. University of Helsinki, February 2019
Salla Merenheimo. Tiedekasvatus: Lasten ja nuorten tutkijakuva – käsityksiä tutkijoista ja heidän työstään. University of Helsinki, January 2019
Ville Hietala. Vertailu eri tekniikoiden yhdistelystä lipopolysakkaridien puhdistamiseksi bakteriofaginäytteistä. University of Helsinki, May 2018
Anne Ries. Structural analysis of the Thermus virus P23-77 capsid. Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, Germany, August 2017
Riia Järvi. Phosphorylation analysis of measles matrix, nucleo and phosphoprotein by phosphate affinity gel electrophoresis. University of Helsinki, August 2015
Pezhman Mohammadi. Three-dimensional reconstruction of Nora-virus by cryo-electron microscopy. University of Eastern Finland, August 2013
Salvatore di Girolamo. Development of an expression and purification strategy of STIV2 proteins. Universita Degli Studi Di Palermo, December 2011
Annuciato Pennino. Studies on the turreted archaeal icosahedral virus STIV2. Universita Degli Studi Di Palermo, February 2010
Heini Hyvönen. Structure of Coxsackievirus A7 using electron cryomicroscopy and a CCD camera. University of Helsinki, April 2008
Pasi A. Laurinmäki. Cryo-EM structure of bacteriophage Bam35 -evolutionary conservation of virus architecture. University of Jyväskylä, May 2006
Jani Seitsonen. Cryo-EM structure of human parechovirus. University of Helsinki, May 2006
Violeta Manole. Molecular studies on the vertex proteins and polymerase of three bacteriophages. University of Bucharest, June 2005
BSc Theses
Naiara Hurtado. February 2021
Alma Seppälä. Haiman coxsackievirus B4 infektiot ja niiden vaikutus tyypin 1 diabetekseen, University of Helsinki, August 2019
Minna Hokkanen. Ihmisen kantasoluja hyödyntävän keksinnön patentoittavuus erityisesti Euroopan unionin tuomioistuimen ratkaisukäytännön valossa. University of Helsinki, January 2017
Emilia Korhonen. Mycobacterium tuberculosis – bakteerin resistenssi riflampisiinille. University of Helsinki, October 2016
Hermanus M. Ansink. Cryo-electron microscopy studies on Chloroflexus aurantiacus chlorosomes. Van Hall Institute, Leewarden, The Netherlands, June 2007
Open datsets for micrographs, electron densities and atomic coordinates
2022
10.2210/pdb8AT5/pdb
10.2210/pdb8AW6/pdb
10.2210/pdb8AXX/pdb
10.6019/EMPIAR- (Domanska et al to be submitted after DOI of paper is issued)
10.2210/pdb7Z51
10.6019/EMPIAR-11032
10.6019/EMPIAR-11014
2021
10.2210/pdb6ZCL/pdb
10.2210/pdb6ZMS/pdb
10.2210/pdb6ZCK/pdb
10.6019/EMPIAR-10652
2020
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2001